Molecular dynamics simulation of the nanosecond pulsed electric field effect on kinesin nanomotor

Jiří Průša,Michal Cifra

doi:10.1038/s41598-019-56052-3

Abstract

Kinesin is a biological molecular nanomotor which converts chemical energy into mechanical work. To fulfill various nanotechnological tasks in engineered environments, the function of biological molecular motors can be altered by artificial chemical modifications. The drawback of this approach is the necessity of designing and creating a new motor construct for every new task. We propose that intense nanosecond-scale pulsed electric field could modify the function of nanomotors. To explore this hypothesis, we performed molecular dynamics simulation of a kinesin motor domain docked on a subunit of its microtubule track - a single tubulin heterodimer. In the simulation, we exposed the kinesin motor domain to intense (100 MV/m) electric field up to 30 ns. We found that both the magnitude and angle of the kinesin dipole moment are affected. Furthermore, we found that the electric field affects contact surface area between kinesin and tubulin, the structure and dynamics of the functionally important kinesin segments, including microtubule binding motifs as well as nucleotide hydrolysis site which power the nanomotor. These findings indicate that external intense nanosecond-scale electric field could alter kinesin behavior. Our results contribute to developing novel electromagnetic methods for modulating the function of biomolecular matter at the nanoscale.

Highlights

Kinesin is a biological molecular nanomotor which converts chemical energy into mechanical work
It was demonstrated that ADP state has a lower contact surface area with tubulin compared to adenosine triphosphate (ATP) and APO state[46] (Fig. S4 therein) which is corroborated by experimental observations that ADP kinesin requires a lower external force to be detached from tubulin than the ATP state[48]
We set up molecular dynamics simulations with no electric field (EF) applied as a control and 100 MV/m EF applied towards the minus and plus end of the microtubule track (Y and −Y directions, respectively) as well as parallel and antiparallel to the dipole moment of the kinesin motor (X and −X directions, respectively)

Summary

Introduction

Kinesin is a biological molecular nanomotor which converts chemical energy into mechanical work. We propose that intense nanosecond-scale pulsed electric field could modify the function of nanomotors To explore this hypothesis, we performed molecular dynamics simulation of a kinesin motor domain docked on a subunit of its microtubule track - a single tubulin heterodimer. We found that the electric field affects contact surface area between kinesin and tubulin, the structure and dynamics of the functionally important kinesin segments, including microtubule binding motifs as well as nucleotide hydrolysis site which power the nanomotor These findings indicate that external intense nanosecond-scale electric field could alter kinesin behavior. While it is acknowledged that kinesin is an electrostatic nanomachine[16], there is no molecular dynamics simulations work investigating the effect of external EF on kinesin nanomotor so far To fill in this gap, we focus in this paper on how EF affects kinesin motor domain docked on a tubulin in terms of kinesin dipole properties, structure, and dynamics

Methods

Results

Conclusion